| Port details |
- py-MDAnalysis Python library to analyze molecular dynamics trajectories
- 2.3.0_1 science
 =0      2.3.0_1Version of this port present on the latest quarterly branch. - Maintainer: yuri@FreeBSD.org
- Port Added: 2018-05-14 00:15:59
- Last Update: 2023-06-27 19:34:34
- Commit Hash: 3d9a815
- Also Listed In: python
- License: GPLv2
- WWW:
- https://www.mdanalysis.org
- Description:
- MDAnalysis is an object-oriented Python library to analyze trajectories from
molecular dynamics (MD) simulations in many popular formats. It can write most
of these formats, too, together with atom selections suitable for visualization
or native analysis tools.
  ¦  ¦  ¦  ¦ 
- Manual pages:
- FreshPorts has no man page information for this port.
- pkg-plist: as obtained via:
make generate-plist - There is no configure plist information for this port.
- Dependency lines:
-
- ${PYTHON_PKGNAMEPREFIX}MDAnalysis>0:science/py-MDAnalysis@${PY_FLAVOR}
- To install the port:
- cd /usr/ports/science/py-MDAnalysis/ && make install clean
- To add the package, run one of these commands:
- pkg install science/py-MDAnalysis
- pkg install py39-MDAnalysis
NOTE: If this package has multiple flavors (see below), then use one of them instead of the name specified above.
NOTE: This is a Python port. Instead of py39-MDAnalysis listed in the above command, you can pick from the names under the Packages section.- PKGNAME: py39-MDAnalysis
- Package flavors (<flavor>: <package>)
- distinfo:
- TIMESTAMP = 1662095086
SHA256 (MDAnalysis-2.3.0.tar.gz) = 29579433c4ea87048278dc1d4019b52e6a19504162659447be7c79fbdbf508ff
SIZE (MDAnalysis-2.3.0.tar.gz) = 3701615
Packages (timestamps in pop-ups are UTC):
- Dependencies
- NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
- Build dependencies:
-
- py39-numpy>=1.16,1<1.25,1 : math/py-numpy@py39
- py39-packaging>=2.0 : devel/py-packaging@py39
- cython-3.9 : lang/cython@py39
- py39-setuptools>=63.1.0 : devel/py-setuptools@py39
- python3.9 : lang/python39
- Test dependencies:
-
- python3.9 : lang/python39
- Runtime dependencies:
-
- py39-numpy>=1.16,1<1.25,1 : math/py-numpy@py39
- clustalw2 : biology/clustalw
- rdkit>0 : science/rdkit
- py39-biopython>=1.71 : biology/py-biopython@py39
- py39-GridDataFormats>=0.4.0 : math/py-GridDataFormats@py39
- py39-fasteners>0 : devel/py-fasteners@py39
- py39-gsd>=1.9.3 : science/py-gsd@py39
- py39-joblib>0 : devel/py-joblib@py39
- py39-matplotlib>=1.5.1 : math/py-matplotlib@py39
- py39-mmtf-python>=1.0.0 : science/py-mmtf-python@py39
- py39-networkx>=2.0 : math/py-networkx@py39
- py39-scipy>=1.5.0 : science/py-scipy@py39
- py39-seaborn>0 : math/py-seaborn@py39
- py39-six>=1.4.0 : devel/py-six@py39
- py39-tqdm>=4.43.0 : misc/py-tqdm@py39
- py39-setuptools>=63.1.0 : devel/py-setuptools@py39
- python3.9 : lang/python39
- This port is required by:
- for Run
-
- science/py-MDAnalysisTests
Configuration Options:- No options to configure
- Options name:
- science_py-MDAnalysis
- USES:
- compiler:c++11-lang python
- FreshPorts was unable to extract/find any pkg message
- Master Sites:
|
| Commit History - (may be incomplete: for full details, see links to repositories near top of page) |
| Commit | Credits | Log message |
|---|
2.3.0_1
27 Jun 2023 19:34:34
 |
Rene Ladan (rene) |
all: remove explicit versions in USES=python for "3.x+"
The logic in USES=python will automatically convert this to 3.8+ by
itself.
Adjust two ports that only had Python 3.7 mentioned but build fine
on Python 3.8 too.
finance/quickfix: mark BROKEN with PYTHON
libtool: compile: c++ -DHAVE_CONFIG_H -I. -I../.. -I -I. -I.. -I../.. -I../C++
-DLIBICONV_PLUG -DPYTHON_MAJOR_VERSION=3 -Wno-unused-variable
-Wno-maybe-uninitialized -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong
-fno-strict-aliasing -DLIBICONV_PLUG -Wall -ansi
-Wno-unused-command-line-argument -Wpointer-arith -Wwrite-strings
-Wno-overloaded-virtual -Wno-deprecated-declarations -Wno-deprecated -std=c++0x
-MT _quickfix_la-QuickfixPython.lo -MD -MP -MF
.deps/_quickfix_la-QuickfixPython.Tpo -c QuickfixPython.cpp -fPIC -DPIC -o
.libs/_quickfix_la-QuickfixPython.o
warning: unknown warning option '-Wno-maybe-uninitialized'; did you mean
'-Wno-uninitialized'? [-Wunknown-warning-option]
QuickfixPython.cpp:175:11: fatal error: 'Python.h' file not found
^~~~~~~~~~
1 warning and 1 error generated.
Reviewed by: portmgr, vishwin, yuri
Differential Revision: <https://reviews.freebsd.org/D40568> |
2.3.0_1
23 Apr 2023 09:09:58
|
Gerald Pfeifer (gerald) |
*: Bump PORTREVISIONs for math/mpc update to 1.3.1 |
2.3.0
11 Jan 2023 15:58:34
|
Dmitry Marakasov (amdmi3) |
*/*: rename CHEESESHOP to PYPI in MASTER_SITES
PR: 267994
Differential revision: D37518
Approved by: bapt |
07 Sep 2022 21:58:51
|
Stefan Eßer (se) |
Remove WWW entries moved into port Makefiles
Commit b7f05445c00f has added WWW entries to port Makefiles based on
WWW: lines in pkg-descr files.
This commit removes the WWW: lines of moved-over URLs from these
pkg-descr files.
Approved by: portmgr (tcberner) |
2.3.0
07 Sep 2022 21:10:59
|
Stefan Eßer (se) |
Add WWW entries to port Makefiles
It has been common practice to have one or more URLs at the end of the
ports' pkg-descr files, one per line and prefixed with "WWW:". These
URLs should point at a project website or other relevant resources.
Access to these URLs required processing of the pkg-descr files, and
they have often become stale over time. If more than one such URL was
present in a pkg-descr file, only the first one was tarnsfered into
the port INDEX, but for many ports only the last line did contain the
port specific URL to further information.
There have been several proposals to make a project URL available as
a macro in the ports' Makefiles, over time.
(Only the first 15 lines of the commit message are shown above  ) |
2.3.0
02 Sep 2022 06:37:41
|
Yuri Victorovich (yuri) |
science/py-MDAnalysis: Update 2.2.0 -> 2.3.0
Reported by: portscout |
2.2.0
21 Jun 2022 17:26:21
|
Thierry Thomas (thierry) |
science/py-MDAnalysis*: upgrade to 2.2.0
Version 0.19.2 is too old and does not support Python-3.9.
Remark: threadpoolctl is disabled in this port. See
<https://github.com/MDAnalysis/mdanalysis/pull/2950> for the impacts on
performance.
Releases notes at <https://github.com/MDAnalysis/mdanalysis/releases>.
PR: 264716
Approved by: yuri (maintainer) |
0.19.2_2
10 May 2021 20:13:20
|
Thierry Thomas (thierry) |
math/py-matplotlib: chase minimum Python version in dependent ports
Since the previous update changed USES=python from 3.6+ to 3.7+, all
dependent ports must have USES=python:3.7+ as well, otherwise it breaks
the @py36 flavor.
PR: 255347
Reported by: sunpoet |
0.19.2_2
07 Apr 2021 08:09:01
|
Mathieu Arnold (mat) |
One more small cleanup, forgotten yesterday.
Reported by: lwhsu |
0.19.2_2
06 Apr 2021 14:31:07
|
Mathieu Arnold (mat) |
Remove # $FreeBSD$ from Makefiles. |
0.19.2_2
13 Jun 2020 15:05:45
 |
antoine |
Unbreak bulk -a |
0.19.2_2
26 Jul 2019 20:46:57
|
gerald |
Bump PORTREVISION for ports depending on the canonical version of GCC
as defined in Mk/bsd.default-versions.mk which has moved from GCC 8.3
to GCC 9.1 under most circumstances now after revision 507371.
This includes ports
- with USE_GCC=yes or USE_GCC=any,
- with USES=fortran,
- using Mk/bsd.octave.mk which in turn features USES=fortran, and
- with USES=compiler specifying openmp, nestedfct, c11, c++0x, c++11-lang,
c++11-lib, c++14-lang, c++17-lang, or gcc-c++11-lib
plus, everything INDEX-11 shows with a dependency on lang/gcc9 now.
PR: 238330 |
0.19.2_1
29 Jun 2019 10:28:48
|
pkubaj |
science/py-MDAnalysis: fix build
Add USES=compiler:c++11-lang to fix:
cc1plus: error: unrecognized command line option "-std=c++11"
Approved by: mentors (implicit approval) |
0.19.2_1
12 Dec 2018 01:35:36
|
gerald |
Bump PORTREVISION for ports depending on the canonical version of GCC
defined via Mk/bsd.default-versions.mk which has moved from GCC 7.4 t
GCC 8.2 under most circumstances.
This includes ports
- with USE_GCC=yes or USE_GCC=any,
- with USES=fortran,
- using Mk/bsd.octave.mk which in turn features USES=fortran, and
- with USES=compiler specifying openmp, nestedfct, c11, c++0x, c++11-lang,
c++11-lib, c++14-lang, c++17-lang, or gcc-c++11-lib
plus, as a double check, everything INDEX-11 showed depending on lang/gcc7.
PR: 231590 |
0.19.2
11 Nov 2018 22:33:50
|
yuri |
science/py-MDAnalysis: Update 0.19.0 -> 0.19.2
Reported by: portscout |
0.19.0
12 Oct 2018 01:15:43
|
yuri |
science/py-MDAnalysis: Update 0.18.0 -> 0.19.0
Reported by: portscout |
0.18.0
20 Jun 2018 17:05:44
|
mat |
Use PY_FLAVOR for dependencies.
FLAVOR is the current port's flavor, it should not be used outside of
this scope.
Sponsored by: Absolight |
0.18.0
14 May 2018 00:15:32
|
yuri |
New port: science/py-MDAnalysis: Python library to analyze molecular dynamics
trajectories |
As an Amazon Associate I earn from qualifying purchases.